Next-generation sequencing (NGS) technologies - Illumina RNA-seq, Pacific Biosciences isoform sequencing (PacBio Iso-seq), and Oxford Nanopore direct RNA sequencing (DRS) - have revealed the complexity of plant transcriptomes and their regulation at the co-/post-transcriptional level. Global analysis of mature mRNAs, transcripts from nuclear run-on assays, and nascent chromatin-bound mRNAs using short as well as full-length and single-molecule DRS reads have uncovered potential roles of different forms of RNA polymerase II during the transcription process, and the extent of co-transcriptional pre-mRNA splicing and polyadenylation. These tools have also allowed mapping of transcriptome-wide start sites in cap-containing RNAs, poly(A) site choice, poly(A) tail length, and RNA base modifications. The emerging theme from recent studies is that reprogramming of gene expression in response to developmental cues and stresses at the co-/post-transcriptional level likely plays a crucial role in eliciting appropriate responses for optimal growth and plant survival under adverse conditions. Although the mechanisms by which developmental cues and different stresses regulate co-/post-transcriptional splicing are largely unknown, a few recent studies indicate that the external cues target spliceosomal and splicing regulatory proteins to modulate alternative splicing. In this review, we provide an overview of recent discoveries on the dynamics and complexities of plant transcriptomes, mechanistic insights into splicing regulation, and discuss critical gaps in co-/post-transcriptional research that need to be addressed using diverse genomic and biochemical approaches.
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The plasma membrane of lymphocytes is highly compartmentalized in so-called nanodomains or protein islands. Proteins such as Caveolin-1 (pink), tetraspanins (blue) or flotillins (violet) define these protein islands and thereby regulate the functioning of the immune system. In this issue (see pages 2387–2397), Schaffer and Minguet discuss the importance of these protein islands regarding lymphocyte activation and the development of immunopathologies. This cover artwork has been created by Susana Minguet.
Decoding co-/post-transcriptional complexities of plant transcriptomes and epitranscriptome using next-generation sequencing technologies
Anireddy S.N. Reddy, Jie Huang, Naeem H. Syed, Asa Ben-Hur, Suomeng Dong, Lianfeng Gu; Decoding co-/post-transcriptional complexities of plant transcriptomes and epitranscriptome using next-generation sequencing technologies. Biochem Soc Trans 18 December 2020; 48 (6): 2399–2414. doi: https://doi.org/10.1042/BST20190492
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